The ZA CD is invaluable as a starting point. But that crap about pulling wires, that's going too far. If you've got an auto harness, sure, get rid of that. But fishing wires through the whole thing is a bit obscene to me. I don't remember all the details now but there were other things I found that weren't right or incomplete. For instance, having an OBD2 motor you'll need to figure something out about the coolant signal for the dash (sorry if you've already covered that).
If you have any thoughts about painting the bay, do it. One day they will hit critical mass and you'll really want to but it'll be too late. At least take some mineral spirits and clean the whole thing as best as you reasonably can, take all rust areas to bare metal and paint with some rust paint (or even primer/body color).